Eukaryotic genes respond to their environment by changing the expression of selected genes. The question we address here is whether distinct transcriptional responses to different environmental signals elicit distinct modes of assembly of the transcription machinery. In particular, we examine transcription complex assembly by the stress-directed SAGA complex versus the housekeeping assembly factor TFIID. We focus on genomic responses to the DNA damaging agent methyl methanesulfonate (MMS) in comparison to responses to acute heat shock, looking at changes in genome-wide factor occupancy measured by chromatin immunoprecipitation-microchip (ChIP-chip) and ChIP-sequencing analyses. Our data suggest that MMS-induced genes undergo transcription complex assembly sequentially, first involving SAGA and then involving a slower TFIID recruitment, whereas heat shock genes utilize the SAGA and TFIID pathways rapidly and in parallel. Also Crt1, the repressor of model MMS-inducible ribonucleotide reductase genes, was found not to play a wider role in repression of DNA damage-inducible genes. Taken together, our findings reveal a distinct involvement of gene and chromatin regulatory factors in response to DNA damage versus heat shock and suggest different implementations of the SAGA and TFIID assembly pathways that may depend upon whether a sustained or transient change in gene expression ensues.